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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtaacttcttggtgcctgatttcctgatgtacatagtatatagacaactacatttcagaaggaacttcatgctctaaactgcttttcagGACCGATCCAAAGCGTTTAGCTGGGACTCTGAGTACTGAGAATGAGGAATCTTGTACCACCTACAATATGCTTAAG

Basic information

species Zea mays
transcript GRMZM2G058739_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058739_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g10190.1 (Oryza sativa), 3'ss of exon 6
gtgtaacttcttggtgcctgatttcctgatgtacatagtatatag-acaactacatttcagaaggaacttcatgct-ctaaactgcttttcagGACCGATCCAAAGCGTTTAGCTGGGACTCTGAGTACTGAGAATGAGGAATCTTGTACCACCTACAATATGCTTAAG
  |||| ||     | |   |  | ||||  | ||||||  |||| | |  |   ||| |      |||   | || ||| |    | ||||||||| ||||||||||||||||||  ||||||||||||||||||||||||||||| || |||||||| ||||| |||
--gtaattt-----tactctagattctga-attcatagtcaatagtatatttctctttgatgtatgactatctacttctatataattattcagGACCAATCCAAAGCGTTTAGCTGATACTCTGAGTACTGAGAATGAGGAATCTTGCACAACCTACAACATGCTCAAG
















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 107

CAAATTGCGTCATTCTTTATGGATACAATAAATTCTTCTCATAGCTACGCAACTGGTGGCACATCTGCTGGTGAATTCTGgtgtaacttc ... tgcttttcagGACCGATCCAAAGCGTTTAGCTGGGACTCTGAGTACTGAGAATGAGGAATCTTGTACCACCTACAATATGCTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

CAAATTGCGTCATTCTTTATGGATACAATAAATTCTTCTCATAGCTACGCAACTGGTGGCACATCTGCTGGTGAATTCTGgtgtaacttc ... tgcttttcagGACCGATCCAAAGCGTTTAGCTGGGACTCTGAGTACTGAGAATGAGGAATCTTGTACCACCTACAATATGCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

CAAATTGCGTCATTCTTTATGGATACAATAAATTCTTCTCATAGCTACGCAACTGGTGGCACATCTGCTGGTGAATTCTGgtgtaacttc ... tgcttttcagGACCGATCCAAAGCGTTTAGCTGGGACTCTGAGTACTGAGAATGAGGAATCTTGTACCACCTACAATATGCTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 704

CAAATTGCGTCATTCTTTATGGATACAATAAATTCTTCTCATAGCTACGCAACTGGTGGCACATCTGCTGGTGAATTCTGgtgtaacttc ... tgcttttcagGACCGATCCAAAGCGTTTAGCTGGGACTCTGAGTACTGAGAATGAGGAATCTTGTACCACCTACAATATGCTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatatagacaactacatttcagaaggaacttcatgctctaaactgcttttcagGACCGATCCAAAGCGTTTAGCTGGGACTCTGAGTACTGAGAATGAGGAATCTTGTACCACCTACAATATGCTTAAG
                                     ctctaaa  putative branch site (score: 704)
                                            ctgcttttc  CT-rich tract
              tacattt  TA-rich tract